Japan in early April
 

We are planning a trip to Japan in early April and after a little research I think we would like to see the following: 3-4 days in Tokoyo, day trip or overnight in Hakone, 1-2 days in Takayma, day trip or overnight in Kanazna, then 3-4 days in Koyoto. We are traveling from New York. Any comments, recommendations, or problems with the direction or order of itinerary would be appreciated.

It depends on your interests and what you hope to accomplish from your trip. If you are into temples and gardens as I am, then I would allocate 5 days for Kyoto. I also wouldn't do the Hakone region as a daytrip, as you would be spending most of your day on trains. 3-4 days in Tokyo seems okay, again depending on what you want to see and do. I haven't been to Takayama or Kanazawa, so I cannot comment on those. However, your routing looks fine, and depending on whether or not the cherry tree are in bloom, you may see larger crowds.

Kanazna what/where is that? If you mean Kanazawa then it is not a good plan.

Are you flying out of Kansai or Tokyo at the end? How many nights total do you have? Kanazawa is not a day trip, and certainly not a stopover between Takayama and Kyoto. Spend at least 2 nights there so you have at least a day. While many do Hakone as a day trip from Tokyo, it really ends up being an exercise in transportation and you miss the main attraction - hotspring ryokan stay.

If you had 10 nights into Tokyo and out of Kansai or Itami you could do 3 nights Tokyo, 2 nights Kanazawa, option of 1 night Takayama and 4 nights Kyoto or 5 nights Kyoto.

Or 2 Tokyo, 1 Hakone, 2 Kyoto, 1 Takayama, 2 Kanazawa, 2 Kyoto - but that is much too much moving for my taste.

Thank you all for your input. I guess I will fly out of Kansai now that I am now thinking of 4 nights Tokyo, 2 nights in Kanazawa (even though I spelled it incorrectly) and 4 nights in Kyoto. Maybe add a side trip to Takayama if practical. Does this sound like a decent plan to catch the highlights?

That is a good plan. You won't need a JR Pass.

Here is some info on the bus route between Takayama - Shirakawago - Kanazawa.
http://www.japan-guide.com/bus/shirakawago.html

You could spend a night in Takayama and/or a night in Shirakawago, or both, but that would take time away from Tokyo or Kyoto. Keep the two nights in Kanazawa.

Then use hyperdia.com to see the train schedule and travel times between Tokyo and Takayama, Takayama and Kyoto, and Kanazawa and Kyoto to decide if you want to go that route and in what direction.

Tokyo - Takayama - Shirakawago - Kanazawa - Kyoto
Tokyo - Kanazawa - Shirakawago - Kyoto via Kanazawa (skipping Takayama)
Tokyo - Kanazawa - Shirakawago - Takayama - Kyoto

You can see some travel options on the route map at the top of page 3 on this pdf:
http://www.jnto.go.jp/eng/location/rtg/pdf/pg-409.pdf

Note that Ogimachi on that map is Shirakawago (the village in Shirakawa district).

Also, the travel time on that map between Ogimachi/ Shirakawago, and Kanazawa is shown as 2.5 hours, but I think a new road makes it a 1 hour trip.

Thanks mrwunrfi, you provided me with lots of options and info. I guess I still have a lot of work to do.